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Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii)

ABSTRACT: Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii)

PROVIDER: PRJNA417828 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6278180_1.fastq.gz	Fastqsanger.gz
	SRR6278180_2.fastq.gz	Fastqsanger.gz
	SRR6278300_1.fastq.gz	Fastqsanger.gz
	SRR6278300_2.fastq.gz	Fastqsanger.gz
	SRR6278360_1.fastq.gz	Fastqsanger.gz

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Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [SYZLO-EUCGR]

Project description:Finding predictive molecular markers for resistance against Myrtle rust may help to identify resistant plants and provide a means of maintaining Myrtaceae production in nursery, especially for ecosystems restoration purposes. Sequence polymorphism involving in differentiate expressed genes are particularly relevant for disease resistance marker design. We sequenced the transcriptomes of resistant and susceptible individuals of three endemic host species: Arillastrum gummiferum, Tristaniopsis glauca and Syzygium longifolium. The rust phenotype of the individuals of each species was defined as "infected" (considered as susceptible) and "healthy" (considered as resistant). We described here a pre-breeding methodology to find disease resistance markers by combining next-generation sequencing, differential gene expression (DGE) and SNP calling. DGE was conducted in parallel using the only one available sequenced Myrtaceae genome (Eucalyptus grandis) and a de novo assembly transcriptome from each species. The edgeR tests if a gene is DE between “infected” individuals versus “healthy” ones. If the fold change log (FC = infected/healthy) is greater than 0, the gene is thus overexpressed in the infected individuals (considered as susceptible).

2018-11-08 | GSE106749 | GEO

Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [SYZLO-DENOVO]

2018-11-08 | GSE106747 | GEO

Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [ARIGU-EUCGR]

2018-11-08 | GSE106736 | GEO

Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [ARIGU-DENOVO]

2018-11-08 | GSE106735 | GEO

Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [TRIGL-FAR-EUCGR]

2018-11-08 | GSE106746 | GEO

Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [TRIGL-FAR-DENOVO]

2018-11-08 | GSE106741 | GEO

Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [TRIGL-BDS-DENOVO]

2018-11-08 | GSE106738 | GEO

Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [TRIGL-BDS-EUCGR]

2018-11-08 | GSE106740 | GEO

Transcriptome data from three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii).

Project description:The myrtle rust disease, caused by the fungus Austropuccinia psidii, infects a wide range of host species within the Myrtaceae family worldwide. Since its first report in 2013 in New Caledonia, it was found on various types of native environments where Myrtaceae are the dominant or codominant species, as well as in several commercial nurseries. It is now considered as a significant threat to ecosystems biodiversity and Myrtaceae-related economy. The use of predictive molecular markers for resistance against myrtle rust is currently the most cost-effective and ecological approach to control the disease. Such an approach for neo Caledonian endemic Myrtaceae species was not possible because of the lack of genomic resources. The recent advancement in new generation sequencing technologies accompanied with relevant bioinformatics tools now provide new research opportunity for work in non-model organism at the transcriptomic level. The present study focuses on transcriptome analysis on three Myrtaceae species endemic to New Caledonia (Arillastrum gummiferum, Syzygium longifolium and Tristaniopsis glauca) that display contrasting responses to the pathogen (non-infected vs infected). Differential gene expression (DGE) and variant calling analysis were conducted on each species. We combined a dual approach by using 1) the annotated reference genome of a related Myrtaceae species (Eucalyptus grandis) and 2) a de novo transcriptomes of each species.

| S-EPMC6362868 | biostudies-literature

Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [ARIGU-DENOVO]

Project description:Transcriptome analysis using RNA sequencing of three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (Austropuccinia psidii) [ARIGU-DENOVO]

| PRJNA417807 | ENA

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